Hi, Can Jeremy (or anyone else) please give a link raw-data-types.xml they used for Illumina and perhaps the R script that was mentioned in this thread. I have written a perl script to do the splitting so it would be good to compare notes and reach a consensus. Is anyone on the list looking at writing the Java plugin?
Thanks a lot, Steve > I have implemented the incorporation of Illumina data into our BASE > system, along with a raw data importer. Our version requires that the > gene_profile.csv be split up into separate files, which we have done > with an R script. This can also be done manually in excel, or feasibly > in a BASE script. > > Nicklas, how do I share the plugin configurations with others? > > Jeremy > > UCLA Department of Neurology > > On 2/5/07, *Nicklas Nordborg* < [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Emil Lundberg wrote: > > Hi all, > > > > Our site will likely wish to store Illumina array data in BASE 2 > in the > > near future. Sifting through the mailing list archive, this seems > indeed > > possible (based on the post below, from july '06). > > > > My question is has anyone implemented this already (Reha Y.?) and is > > willing to share the specifications and/or will this find its way > into > > BASE 2 proper some day? > > If somebody is willing to implement it. Right now we have to focus on > other things. We can put it into the standard BASE distribution if > someone: > > * comes up with a <raw-data-type> definition for the Illumina Chip > * provides one or more plugin configurations for importing the data > files > > For an example of the existing plugin configurations see: > > http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html > > <http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html> > > /Nicklas > > > > > > > regards, > > > > /Emil > > > > ________________________________ > > Emil Lundberg / Sysadm > > Linnaeus Centre for Bioinformatics > > Uppsala University > > > > > >> Reha Yildirimman wrote: > >> > Hello, > >> > > >> > using Base2 we are trying to implement the Illumina Chip design. > >> In order > >> > to use the raw data files describing coordinates and intensities > >> of probes > >> > there is a need to define a new raw data type besides the > given ones > >> > (affymetrix,agilent,spotfinder,...). > >> > > >> > Is this already implemented, is there a way around the "data > >> type" problem > >> > or am I looking at the wrong spot in base2 ? > >> > >> Yes, you can add raw data types to Base2. You have to find and > modify > >> the file 'raw-data-types.xml '. It should be located in the > >> <basedir>/www/WEB-INF/classes directory. > >> > >> Add a tag <raw-data-type> for the Illumina Chip for example: > >> > >> <raw-data-type > >> id="illumina" > >> channels="2" > >> name="Illumina" > >> table="RawDataIllumina" > >> > > >> > >> Then add as many <property> tags as you need. The last step is > to run > >> the <basedir>/bin/updatedb.sh script to create the new table. > >> > >> /Nicklas > > > > > > > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
